C77,
What type of account do you have?
My understanding of hosting tells me that your host has blown smoke up your …
Apache is installed in its own directory and its httpd.conf file is located in its conf subdirectory. Therefore, creating another httpd.conf in your home directory should have exactly no relevance to anything. Of course, your host might have configured your dedicated server to have YOUR personal Apache install look elsewhere for additional directives but I’ve never heard of that being done (that’s not to say that it can’t be done, simply that it’s illogical on a dedicated and can NEVER be done on a shared server).
IMHO, your host’s support should ensure that your code is in your httpd-vhosts file so it can only impact your account’s domains.
After all that, yes, it should be safe to remove those lines from .htaccess.
To me, the simplest solution would be to leave the content type alone (it’s standard) and add the charset directive in your files section in a meta tag.
Regards,
DK